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iqbal-lab-org / minos

Variant call adjudication
MIT License
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removing perl_generated_vcf caused a bug #76

Closed iqbal-lab closed 5 years ago

iqbal-lab commented 5 years ago

ERROR ~ Error executing process > 'minos_all_small_vars (12)'

Caused by: Process minos_all_small_vars (12) terminated with an error exit status (1)

Command executed:

sample_name=$(cat sample_name.37) minos_outdir=small_vars.minos.37 minos adjudicate --sample_name $sample_name --gramtools_build_dir /hps/nobackup/iqbal/zi/Cryptic_releases/nextflow.work/f2/855ff40b18dd238c529b231e1f7d95/gmtools_build_dir --reads /nfs/leia/research/iqbal/mhunt/Cryptic_production/Pipeline_root/00/00/05/27/527/Pipelines/1/variant_call/0.7.3.ref.3/samtools/rmdup.bam $minos_outdir /nfs/leia/research/iqbal/mhunt/Cryptic_production/Pipeline_refs/3/ref.fa "small_vars_clustered.vcf"

Command exit status: 1

Command output: (empty)

Command error: Traceback (most recent call last): File "/usr/local/lib/python3.6/dist-packages/pyfastaq/utils.py", line 21, in open_file_read f = open(filename) FileNotFoundError: [Errno 2] No such file or directory: '/hps/nobackup/iqbal/zi/Cryptic_releases/nextflow.work/77/f9b9651dc28b949dfcf91257f014f0/gramtools.build_dir/split.0.gramtools_build/perl_generated_vcf'

Work dir: /hps/nobackup/iqbal/zi/Cryptic_releases/nextflow.work/27/fc27423b35372a9638fbed7c3b4976

Tip: view the complete command output by changing to the process work dir and entering the command cat .command.out

iqbal-lab commented 5 years ago

@bricoletc if you have a chance to take a look, i'd appreciate it

bricoletc commented 5 years ago

I think https://github.com/iqbal-lab-org/minos/commit/798a7dfd2a95d44ad8c4b9f4076a60db4cf7f566 fixes this.

bricoletc commented 5 years ago

Confirm this has been fixed as we successfully ran minos adjudicate on 49k Mtb samples